You can alias some of these commands to prevent yourself from having to type long commands over and over again. Access and modify your bash_profile using:

nano ~/.bash_profile

And add an alias like:

alias qu="squeue --user=<your_username>

Running the same command on multiple files.

Say I wish to perform the same MSA on several fasta files. That is, I'd like to run:

mafft input.fasta > output.fasta

A typical example is doing multiple-sequence alignment on all eight gene segments of a flu virus, which exist as eight .fasta files.

You can create a text file with a list of bash commands, and run them all one after another by calling the bash command on that text file. For instance, create a file my_run.txt, containing the following:

echo "first command"
echo "second command"
date

And in your terminal, cd to the place where you've saved my_run.txt and do:

bash my_run.txt

This will print out "first command", "second command", and today's date.